Although the comparison of relevant scales of variation is a prerequisite for understanding processes structuring benthic communities, deep-sea studies have traditionally examined spatial patterns of distribution of assemblages along a single scale or environmental gradient. A multiple-scale approach identifying which spatial-scale and associated environmental gradient is the most important in structuring the deep-sea benthos has never been attempted. To answer this question this study merged three independent data sets of nematodes from the Arctic deep seas. The data set included 300 samples and covered both margins of the Arctic Seas (Greenland and Norway–Spitsbergen, ca. 103 km distant apart), seven degrees of latitude (72–79°N), 2700 m depth differences (656–3350 m), horizontal distances between cores (20 cm) and vertical distances within the uppermost sediment layers (1–5 cm). Results showed that for abundance (N) and generic composition, differences between margins (M) and between cores (C) were the most important sources of variability, followed by water depth (D), vertical distribution within the sediment (VD) and latitude (L). For species and genera diversity, measured as ES(50) and EG(50), the order was slightly different. For species, C was the most important source of variability, followed by D, M and L, while for genera VD was the most important. Relationships between environmental variables and the fauna were highly dependent on scale indicating that, at least for the deep-sea environment, we cannot predict the structure of nematode assemblages by scaling up or down results obtained on one or another scale. The only consistent pattern across different spatial scales was that higher abundances were associated with higher number and lower turnover of species. This raises the hypothesis that the most abundant species are also the most widespread and that abundance is the best predictor of nematode diversity patterns in deep-sea ecosystems.